Compilation error of 5.2.x related to libxc

[Franz Fischer]

Hi all,

I am experiencing quite some weird behaviour when compiling yambo.
I had a yambo version 5.2.0 working for quite some time on my universities hpc facility and I compiled it myself some time ago.
Now that we had a hardware issue that deleted all user related software packages I wanted to recompile yambo with the exact same configure options as last time, namely:

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./configure CC=mpiicc FC=mpiifort --enable-mpi --enable-hdf5-p2y-support
make core

My compilation fails at the libxc step spitting out these lines:

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\t[libxc-5.2.3] download

gzip: stdin: not in gzip format
tar: This does not look like a tar archive
tar: Exiting with failure status due to previous errors
gtar: This does not look like a tar archive
gtar: Exiting with failure status due to previous errors
WARNING: I can't seem to be able to run `tar' with the given arguments.
         You may want to install GNU tar or Free paxutils, or check the
         command line arguments.
\t[libxc-5.2.3] installation
/bin/sh: line 0: cd: libxc-5.2.3: No such file or directory

The compilation finally fails when trying to include the libxc library:

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make[2]: *** [mod_xc_functionals.o] Error 1
mod_xc_functionals.f90(29): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [XC_F03_LIB_M]
mod_xc_functionals.f90(180): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [XC_F03_LIB_M]
\t[driver] yambo (setup)
yambo linking failed. Check log/compile_yambo.log
mod_xc_functionals.f90(29): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [XC_F03_LIB_M]
mod_xc_functionals.f90(180): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [XC_F03_LIB_M]
make[1]: *** [yambo] Error 1
yambo build failed

I would be really happy if you could tell me what I can try to fix that. I will also attach the configure.log and the compile_yambo.log.

Thanks in advance.

Best,
Franz

[Nicola Spallanzani]

Dear Franz,
unfortunately, the issue is related to changes in the repository of the libxc libraries. Currently, it can be solved by the patch I'm sending you. I recommend downloading the YAMBO sources from GitHub and then applying the patch using git:

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git clone https://github.com/yambo-code/yambo.git
cd yambo
git checkout 5.2.3
git apply libxc.patch.txt

As soon as possible, we will create a new release including the patch.

Best,
Nicola

[Franz Fischer]

Hi Nicola,

I tried what you suggested, but I am still experiencing some issues.

The installation step of libxc library still seems to fail, I am getting this in the make step:

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\t[libxc-5.2.3] download
\t[libxc-5.2.3] autoreconf
\t[libxc-5.2.3] configuration
\t[libxc-5.2.3]  compilation
\t[libxc-5.2.3] installation
chmod: cannot access ‘/usw/bbb2414/codes/yambo/lib/external/intel/mpiifort/lib*/*xc*a’: No such file or directory

Maybe just a typo in the chmod command?

and then the compilation breaks at this:

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make[2]: *** [mod_xc_functionals.o] Error 1
mod_xc_functionals.f90(13): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [XC_F03_LIB_M]
mod_xc_functionals.f90(164): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [XC_F03_LIB_M]
\t[driver] yambo (setup)
yambo linking failed. Check log/compile_yambo.log
mod_xc_functionals.f90(13): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [XC_F03_LIB_M]
mod_xc_functionals.f90(164): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [XC_F03_LIB_M]
make[1]: *** [yambo] Error 1
yambo build failed

Any further help would be nice!
Thanks again.

Best,
Franz

[Daniele Varsano]

Dear Franz,

it could be useful to have a look to:
./log/compile_libxc-5.2.3.log

to check what went wrong with the libxc installation.

Best,
Daniele

[Franz Fischer]

Hi Daniele,

see all the libxc related logs attached.

Best,
Franz

[Daniele Varsano]

Dear Franz,

it seems that libxc are correctly downloaded, but then the configure file to install them is not present. I do not know why this is happening.
Can you try to do a
>make distclean
and try again?

Best,
Daniele

[Franz Fischer]

Hi Daniele,

I experience the same issues after doing:

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make distclean

During compilation I see these lines again:

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\t[libxc-5.2.3] download
\t[libxc-5.2.3] autoreconf
\t[libxc-5.2.3] configuration
\t[libxc-5.2.3]  compilation
\t[libxc-5.2.3] installation
chmod: cannot access ‘/usw/bbb2414/codes/yambo/lib/external/intel/mpiifort/lib*/*xc*a’: No such file or directory

and then the build fails:

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make[2]: *** [mod_xc_functionals.o] Error 1
mod_xc_functionals.f90(13): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [XC_F03_LIB_M]
mod_xc_functionals.f90(164): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [XC_F03_LIB_M]
\t[driver] yambo (setup)
yambo linking failed. Check log/compile_yambo.log
mod_xc_functionals.f90(13): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [XC_F03_LIB_M]
mod_xc_functionals.f90(164): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [XC_F03_LIB_M]
make[1]: *** [yambo] Error 1
yambo build failed

When inspecting the

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~/log/autoreconf_libxc-5.2.3.log

it says:

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/bin/sh: autoreconf: command not found

Also, the configure script does not seem to be in the libxc directory:

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/usw/bbb2414/codes/yambo/lib/libxc/libxc-5.2.3

Is there anything else I could try?

Best,
Franz

[Franz Fischer]

Hi all,

I actually found the error when trying to compile libxc on my own.

The issue was that I had to load some modules on my hpc, namely:

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module load autoconf/2.69
module load automake/1.16.1
module load libtool/2.4.6

in order to generate the ./configure.sh file needed to configure libxc.

After that everything worked like a charm and I compiled yambo 5.2.3 using:

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git clone https://github.com/yambo-code/yambo.git
cd yambo
git checkout 5.2.3
git apply libxc.patch.txt

./configure CC=mpiicc FC=mpiifort --enable-mpi --enable-hdf5-p2y-support

make core

For completeness, I also tried to compile yambo without

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git apply libxc.patch.txt

, but this was still raising the error from the beginning of this post.

Thank you all for your help.

Best,
Franz

[Daniele Varsano]

Dear Franz,

the patch is needed to download the libxc as they recently changed the repository address.
From what you say, it could be enough to install the autoconf package in your machine:

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sudo apt-get install autoconf

and then try again to compile. Hopefully this should solve the problem.

Best,
Daniele

[AzulineSky]

Hello,

I still have the same error as Franz.

\t[libxc-5.2.3] installation
chmod: cannot access ‘/home/magr4985/Apps/yambo/lib/external/intel/mpiifort/lib*/*xc*a’: No such file or directory

The config_libxc-5.2.3.log shows the following message:

checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... configure: error: newly created file is older than distributed files!
Check your system clock

What can I do when this happens?

Thanks for your help!

Best regards,
Max